Council On Dairy Cattle Breeding Navigation Guide For .
Council on Dairy Cattle BreedingNavigation guide for NominatorsLatest update: October 24th, 20171 Page
Contents1. Data Flow and Exchange . 41.1 Report Cards . 41.2 Dynamics of Data Flow . 51.3 Data Flow between Nominators and CDCB . 61.4 Steps to Receive Evaluation Results from CDCB . 71.5 Data Exchange through secure FTP . 82. Fee Code information . 92.1 How CDCB Collects Fees through Genomic Nominators . 93. Nomination . 103.1 Nomination information . 103.2. Nomination Through WebQuery . 103.3. Nomination Through secure FTP (SFTP) . 123.3. Format 1 and Format 1G . 134. Common Reasons for not receiving an Evaluation (and How to Correct errors) . 154.1 Where to Find Genomic Conflicts . 154.2 Common reasons for not receiving an evaluation. 16Genotype was not usable due to a conflict, low call rate, being a crossbred (PI “B”) . 16The genotype became usable after the genotypes were extracted for the evaluation . 16The breed of evaluation is not among those we generate evaluations for . 17The animal’s genotype conflicted its imputed dam . 18The fee code is “N (No fee paid)” or “H (Historic)” . 18The bull has semen marketed and it’s not a triannual evaluation release . 18The owner of the bull is not located in the US and AI service fee has not been paid, so theevaluation is not public . 18The genotype is designated parentage verification only (PI “P”) . 19The bull is foreign, over 15months of age and no AI service fee has been paid. 19Wrong animal ID . 195. Web Queries. 205.1 What is Web Query and what can we do with it . 205.2 CDCB-Nomination Q . 205.3 Affiliate specific genotype reports . 205.4 Check FMT1 records . 222 Page
5.5 Check Dam . 225.6 Get 116 parentage SNP for a list of animal IDs . 245.7 New Genotype Query . 245.8 GT Fee . 255.9 parentage.cfm. 255.10 Genotype Move/Swap APP . 255.11 getfee . 266.Genomic Nominator Checklist . 273 Page
1. Data Flow and Exchange1.1 Report CardsReport Cards are made available to genomic nominators on a monthly basis. They provide summarystatistics from the genotypes submitted by each genomic nominator. Since the data available in thedifferent situations is different, not all metrics are considered strictly (herds with registered cattleusually have more accurate pedigree data than non-registered herds with commercial orientation).1. Total genotypes. Determined by monthly release dates.2. Number of genotypes for each chip type.3. Genotypes missing nomination when loaded. Nominators are required to submit anomination for each animal before the genotype is submitted to the CDCB collaboratordatabase, as stated in the Quality Certification Requirements for Genomic .4. Genotypes with unknown animal ID (Identification). This occurs when the animal has notbeen nominated and the genotype submission: i) does not contain animal ID information,or; ii) the animal ID has not been entered in the CDCB collaborator database.5. Sires pedigree missing. Frequency of missing sire ID information in the CDCB database.Common reasons are: the sire ID provided is invalid, a herd bull is not enrolled with a breedassociation, or a foreign bull’s pedigree has not been provided. It’s nominator responsibilityto provide this information.6. Dam pedigree missing. Frequency of missing dam ID information in the CDCB database.7. Dam blanked due to conflict. Dam ID was provided but the information was not stored dueto a conflict. Common reasons are: the animal’s birth date did not agree with the dam’scalving date, a maternal sibling has a birth date within 9 months of the animal submitted,etc. These checks are bypassed for animals coded as having resulted from an embryotransfer birth.8. IDs with 573/574. Numeric IDs starting with these digits are assigned by the nominator andtypically not attached to the animal. The preferred solution is to identify the animal by a tagattached to the animal.9. Group name not found in fee table for codes 1 or 2. The DHI herd code supplied was notfound among the herd codes that have a fee code assigned. This can be expected to occurfor those herds that have begun testing recently.10. Group name not found as a herd of the animal or dam. The herd code assigned by thenominator does not agree with the one in the CDCB collaborator database, which camethrough DHI.11. Genotypes not usable due to conflicts. Genomic conflicts are results of incorrect data, suchas incorrect pedigree, identification, breed code, sex etc. Therefore this frequency of thegenomic conflict inversely related to accuracy of submission.4 Page
12. Genotypes with fee code N A complete nomination requires assignment of fee code,therefore no nomination should be left with fee code N.13. Genotypes with assignment to animal changed A genotype reassignment indicatesincorrect indication of pedigree/nomination. This report shows number of genotypes thatwere reassigned during the month.14. Animals with a change in sire or dam Changing a sire/dam indicates incorrect pedigree. It isnominator’s responsibility to ensure correct pedigree.Example of a report card:1000,Total genotypes for NOMINATORX for YYMM130,CHIP 1870,CHIP 24,Genotypes missing nomination when loaded1,Genotypes with unknown animal ID5,Sire pedigree missing926,Dam pedigree missing22,Dam blanked due to conflict5,IDs with 573/57412,Group Name not found in fee table for fee codes 1 or 29,Group Name not found as a herd of animal or dam16,Genotypes not usable due to conflicts22,Genotypes with fee code N13,Genotypes with assignment to animal changed84,Animals with a change in sire or dam1.2 Dynamics of Data FlowThere are 5 categories of organizations that interact with the CDCB collaborator database:Purebreed Dariy Cattle Associations (PDCA), Dairy Records Processing Centers (DRPC), DairyRecord Providers (DRP), National Association of Animal Breeders (NAAB) and severalinternational partners. Once each organization submits their data, it is first quality checked andgood records are loaded into the CDCB collaborator database. The data is then used to obtainand provide a plethora of CDCB services, including genetic and genomic evaluations. Thediagram below summarizes the data flow:5 Page
1.3 Data Flow between Nominators and CDCBThe following diagram describes specifically the role of Genomic Nominators in data exchangeswith the CDCB collaborator database.6 Page
The process starts with the decision of a dairy producer or a company (e.g. a stud) to obtain agenomic evaluation from CDCB. The Genomic Nominator has a key role in transforming thisdecision into an actual service. It manages the collection of biological samples and ensures theyare sent to one of the CDCB certified laboratories with the complete and correct information. Itnominates the animal before the genotype arrives at CDCB. It is important to stress this:Genomic Nominators are required to complete the nomination process before CDCB receivesthe genotype, as the pedigree is an essential part of the QC process of the genotype.Nomination can be done through a web application (https://queries.uscdcb.com/CFqueries/Nom2.cfm - PASSWORD PROTECTED) or by submitting format1G to the GenomicNominator “in” directory in the CDCB sftp area.Once both nomination and genotype submission steps are successfully completed and allconflicts/errors have been eventually corrected, the genomic nominator will receive a first nonofficial weekly evaluation and monthly official evaluation results. As listed in the “Corerequirements for Genomic Nominators” in the Quality Certification Requirements for GenomicNominators (https://redmine.uscdcb.com/documents/8), the nominator is expected to deliverthe results to the herd/stud originally requesting CDCB services.1.4 Steps to Receive Evaluation Results from CDCB1. The genomic nominator collaborates with a producer and a CDCB approved GenotypingLaboratory to arrange the biological sample collection and submission to the lab. The GenomicNominator is responsible that all information correlated with the sample is accurate andcomplete.2. Before the samples are genotyped and submitted to the CDCB collaborator database, thegenomic nominator is expected to complete the nomination process. Nominations can becompleted on a web query or in batch (i.e. multiple nominations done contemporarily), throughthe submission of a format1G service/wiki/Format 1) to the “in” folder of the CDCB SFTP area (ftp.uscdcb.com). In this lattercase, typically a “notify” file is generated in the “out” directory. The nominator is expected tocheck this file: it contains the outcome of the nomination and linked information.3. After the genotype is loaded into the CDCB collaborator database, genotypes with errors arereported back in the “out” folder of the CDCB sftp area. The “genomic error” file contains alarge number of information that the genomic nominator should use to correct the errors. Onlygenotypes flagged as “usable” with complete nomination (and fee code assigned) qualify toreceive CDCB evaluations.4. New individuals will obtain a non-official weekly evaluation (released on the next Tuesday inthe “out” directory after the genotype became usable). These animals will receive officialmonthly evaluations every month as long as their genotype is flagged as “usable”.5. Nominators are responsible to distribute the results back to the producer.6. Nominators will receive the initial fee invoice from CDCB, based on the fee code assigned. AIservice fee for males being marketed using US genomic evaluations should be paid to NAAB.7 Page
1.5 Data Exchange through secure FTPCDCB and genomic nominators can exchange data through the CDCB web query system orthrough a secure FTP area. The web query is typically used when processing a small number ofrecords or few records need to be displayed. However, when large number ofanimals/genotypes need to be processed, this typically is done through batch submissions. Filesproduced by CDCB are placed in the “out” directory. Files submitted by genomic nominators areplaced in the “in” folder”.A full description of the files generated by CDCB and placed in the “out” folder is available rservice/wiki/CDCB general files distributed to nominators .8 Page
2. Fee Code information2.1 How CDCB Collects Fees through GenomicNominatorsThe CDCB genomic fees are structured to reward producers that are providing the most data orinformation for the greatest value to the CDCB cooperator database. The current fee scheduleencourages contributors to not only maintain, but to increase the amount and kinds of datathey are contributing to the system, to improve accurate genetic evaluations.All required Initial Fees are to be collected by the genomic nominator. The AI Service Fee iscollected by NAAB. All fees collected will be then be forwarded to the CDCB. The female andinitial male fees will be charged only to the first genotype submitted for the animal.There will be no refund of fees, except for errors generated by CDCB. Even if the genomic testresults do not work to the submitter’s satisfaction or a male is not placed into service.The detailed information is described in DCB-Fee-Schedule-Update-7-15-2016.pdf. The CDCB has two onlineapplications (GT Fee: https://queries.uscdcb.com/CF-queries/GT Fee.cfm [PASSWORDPROTECTED] and getfee: https://queries.uscdcb.com/CF-queries/getfee.cfm [PASSWORDPROTECTED]) to help genomic nominators determining the appropriate fee codes (details in 6.Nomination and Data Correction Using Web Query). The CDCB has also created an applicationtool “CDCB Fee Schedule”: https://www.uscdcb.com/fs 01/ to help genomic nominatorsdetermining the appropriate fee codes. Finally, on the day prior to the monthly genomicrelease, CDCB places file NOMNAME Check Fee Code 1705.csv in the “out” directory of eachgenomic nominator to show the fee assigned to each individual genotyped. This file is reviewedby CDCB staff and forwarded to the CDCB treasurer who then prepares the invoice, which isthen sent to the genomic nominator.9 Page
3. Nomination3.1 Nomination informationNomination is one of the most important data CDCB receives from its clients. Nomination is aprocess where a series of critical information is included in the CDCB collaborator database: Pedigree of the animal (if the pedigree is not in our database already): The pedigree ofan animal is important not only for the evaluation itself but also to check for parentprogeny conflicts during genotype submission. Without knowing the parentage, we arenot able confirm that the genotype is from the intended animal. This is the one of thereasons why nomination should be completed before submission of genotypes.Association between the sample ID and the Animal ID: Association between sample IDand the animal ID is extremely important. Missing association will not allow linking thegenotype to the correct animal (event also known as “genotype with zero key”).Providing the correct fee code: The correct fee code is required, in order to fairly chargefor the evaluation. Failing to indicate the fee code will leave the fee code “N”, whichmeans “no CDCB prediction will be delivered, and no fee imposed”.Providing correct parentage indicator: The parentage only indicator is necessary todetermine the type of service required. If parentage only code is determined, there willbe no fees billed to the nominator (and no other service released). 3.2. Nomination Through WebQueryThe CDCB web query called CDCB-Nomination Q can be used when the animal’s pedigree isalready in the CDCB collaborator database (e.g. the animal is in a DHI herd, or is a registeredanimal1).1)2)3)4)Go to the Animal Queries: https://queries.uscdcb.com/loginLog in using your credentials. Accept the “Terms of Use”Choose the CDCB-Nomination Q put Nominator ID (if needed), Parentage Indicator (PI), Group/Herd ID, Fee Type, Animal ID,and Sample ID in each designated box like above and click submit.(Parentage Indicator and Fee Type (code) are explained r-service/wiki#COMMONLY-USED-CODES)1It is unlikely a pedigree is in the CDCB collaborator database if the animal is registered with a foreign breedassociation other than Canada10 P a g e
5) If the animal’s pedigree already exists in the CDCB collaborator database, parentage and theanimal’s nomination status are displayed as below. If the genomic nominator confirms thenomination information is all correct, then by just clicking “Add This NEW Record” button, thenomination is completed.6) If the animal’s pedigree is not in the CDCB collaborator database, the following message will bedisplayed. By clicking on “Request pedigree from non-CDCB source”, prompts a request to findthe animal’s pedigree from external sources, such as breed associations or Interbull. Thereturned outcome (if any) can be accepted – and the nomination process completed - bycompiling the information and clicking on “Submit Format 1g”.11 P a g e
7) If the external research of the animal’s pedigree failed, the genomic nominator will have tosubmit a Format1 through to the CDCB sftp area.8) Most of the information displayed can be updated/corrected. Please be aware that no changesto fee code are allowed once an evaluation has been released. For example, the “SOLDfunction” allows changing the requesterID after nomination is completed. However, pleasenote that only the current nominator can perform that change. An Email will be sent to the newnominator, to notify the change.3.3. Nomination Through secure FTP (SFTP)When a large number of animals need to be nominated, submission through SFTP isrecommended.The process is automated in the CDCB system. The genomic nominator should simply place aFormat1/Format1G file in the “in” directory of his SFTP area. In order to be recognized, the fileshould be named according to the following conventions: For Format1, files should be named as YYYYMMDD.1X, where YYYYMMMDD is theyear,month and day (e.g. 20170101) and X can be either a letter or number.For format1G, files should be named as YYYYMMDD.1GX.Once the submission is processed, a “notify” file (notify.YYYYMMDD.1(G)X) is placed in the “out”directory. This file contains information of errors and the status of the submission. In case of a1G file, it contains information on the success (or not) of the nomination process.12 P a g e
3.3. Format 1 and Format 1GFull information on Format1 format is available at: ervice/wiki/Format 1Format1 is the CDCB standard for a pedigree record. Format1 consists of the animalidentification, sire identification, dam identification and cross reference identification, inaddition to some other information, such as birthdate, source code, and multiple birth code.Ex) Format1 for ELLA DEW SUGAR PIE ETFormat1G is a Format1 that includes nomination data. A Format1 becomes a Format1G byplacing a “G” at byte position 88 and by including nomination information: sampleID @54-70GroupID @130-137Parentage Indicator @138fee code @139Herd code difference reason code @140 (if applicable) .Ex) 173A1B2C3D4E5F6SUGAR PIE ET13 P a g e35051162N220160219B20160312G013HR000000BELLA DEW
CDCB staff has received multiple requests for clarifications on the following fields for Format1and Format1G:Record Source Code (@79) - ervice/wiki/Source code : Source code is used to prioritize the data submitted. Since CDCB canreceive multiple records for one animal from different organizations, the system prioritizes thedata depending on the submitter. An organization whith lower priority cannot correct recordsmanaged by a higher priority source code (“B” has the highest priority among all organizations).Record Type Code (@88) - ervice/wiki/Record type code : Record type code is used to indicate how the record should beprocessed by the CDCB system. Since Format1 can contain different types of information,indication of record type is necessary. So by assigning Record Type code, genomic nominatorscan add/delete/change the information currently stored in the CDCB collaborator database.Multiple Birth Code (@91) - ervice/wiki/Multiple birth code : Multiple Birth Code (MBC) should indicate the type of birthof the animal. This information is used to verify the relationship with its sire, dam and siblings.14 P a g e
4. Common Reasons for not receiving anEvaluation (and How to Correct errors)There are a number of possible reasons that prevent genomic nominators from receiving agenetic evaluation on the animals. The two most common cases are: A) the genotype of theanimals is not flagged as “usable”, meaning there are conflicts preventing the CDCB system touse the genotype, and; B) the nomination is not complete (fee code is set to “N”), meaning thenomination was not completed successfully. In this section, the genomic nominators will founda set of useful information to prevent that from happening.4.1 Where to Find Genomic ConflictsDuring the genotype loading process, the CDCB system checks the quality of the data, such asparent-progeny conflicts, Hardy–Weinberg equilibrium, missing information, and (many) more. Italso generates report files to inform genomic nominators on what should be corrected for thegenotype to be flagged as “usable”. As discussed before, it is one of genomic nominator’sresponsibilities to make the genotype usable.Once a CDCB genotyping laboratory loads a batch of genotype data, genomic nominatorsreceive a .zip file named LAB YYYYMMDDXX.NOM.zip (ex. GSek 20170426A1.ABS.zip). The fileis placed in the genomic nominator “out” directory. The .zip file contains some or all of thefollowing files: NOM Nominator Report.csv: Reports on number of errors/conflictsNOM Genomic conflicts.htm: Animals with error codes (web version)NOM Genotype Conflicts.csv: Animals with error code (csv version)NOM Parentage.csv: Parentage informationBB LABCHIPYYYYMMDDX No Nomination.csv: animals with missing informationNOM PGS unlikely.csv: Unlikely PGS (if any)The file called “NOM Genotype Conflicts.csv” contains a maximum of 6 error codes for eachsample. Animals rarely have more than 6 conflicts, but it is common that multiple errors existsfor one sample including errors related to its parents, siblings, and grandparents.Columns named “code[1-6]” indicate the error codes describing the conflict(s) detected for thegenotype (documented in: 15 P a g e
service/wiki/Genomic error codes ). Columns named “ID[1 – 6]” are the ID(s) related to thoseerrors and conflicts.The NOM Genomic conflicts.htm (web browser friendly) contains the same information but ona more human-friendly view.4.2 Common reasons for not receiving an evaluationGenotype was not usable due to a conflict, low call rate,being a crossbred (PI “B”)Genomic conflicts are definitely the main reasons that prevent an animal from obtaining anevaluation (even when the nomination was done correctly). Resolving these conflicts is one ofthe most important roles of genomic nominators. Therefore, it is very important for nominatorsto understand the meaning of conflicts/errors reported and how to fix them in order to makethe genotype usable for CDCB evaluations. Full documentation on these errors can be found r-service/wiki/Genomic error codesAs for the SNP-based test to detect crossbreds, documentation of the current thresholds isreferenced erservice/wiki/CDCB Genomic Dictionary#Breed-conflict-determinationThe genotype became usable after the genotypes wereextracted for the evaluationCDCB releases 3 types of evaluations: weekly, monthly, and triannual evaluations.It is important that genomic nominators make the necessary corrections to their data beforethe cutoff deadline. The link below provides deadlines and release dates for CDCB sched.cfm)16 P a g e
Weekly evaluationsA weekly evaluation is not an official evaluation. The purpose of a weekly evaluation is to helpproducers in making quick mating, culling, and marketing decisions.The data must be loaded by 6:00 pm on Sunday. CDCB Genotyping Laboratories have to submittheir data earlier than that, as substantial processing time is required to control large files. Inthis evaluations, only animals having a usable genotype for the first time before the deadlinewill be included. No further weekly evaluation is provided after the first one was released. Theresults are released every Tuesday at 8:00 am.Monthly evaluationThe monthly evaluation is official. All qualifying genotyped animals are included. No updates inthe phenotypic records are applied. The cutoff for the monthly evaluation is on Sunday at 6:00pm after the genotype submission correction week and the release day is the first Tuesday ofthe month (might be different during the months of triannual evaluations are released) at 8:30am.Triannual EvaluationThe triannual evaluations are official and are released 3 times a year: April, August, andDecember. Unlike the first two evaluation types, this evaluation includes new phenotypic data.All animals, genotyped or ungenotyped, are distributed. The updated traditional evaluationsare an input to the genomic evaluation system.The breed of evaluation is not among those we generateevaluations forWe currently calculate (G)PTAs for 5 breeds: Ayrshire, Brown Swiss, Guernsey, Jersey, andHolstein. To ensure as much as possible to provide accurate evaluation results to producers,CDCB performs an approximate breed check for all genotyped animals when their genomic datais processed. The system checks that the breed declared in the sample is the breed with thefewest unlikely breed specific alleles. Animals failing this check, still can be included in theevaluations if their BBR (Breed Base Representation) values are higher than 90% for thedeclared breed. However, since this value is obtained during the evaluation of other animals,the evaluation for animals failing the approximate SNP test, but passing the BBR threshold willbe distributed the week after.17 P a g e
The animal’s genotype conflicted its imputed damSince 2016, genomic nominators have been notified when an animal’s genotype has a conflictwith its dam’s imputed genotype. Unless the conflict is fixed, this animal with the conflict willbe excluded from our evaluations.The “affiliate specific genotype reports” allow all genomic nominators to obtain a list of theseanimals at any given time.The fee code is “N (No fee paid)” or “H (Historic)”Fee code “N” means that no payment of a fee has been indicated for the animal. It will not beevaluated until a different fee code is assigned to the animal.If a fee code is indicated as H, then the animal is designated as historical. These animals withfee code “H” are used in the reference population to increase accuracy of estimates, but thoseanimals do not receive an evaluation.Reference on available fee codes: ervice/wiki/Genomic fee codesThe bull has semen marketed and it’s not a triannualevaluation releaseFor bulls being marketed, the evaluation is updated only for the triannual evaluation: on April,August, and December.The owner of the bull is not located in the US and AI servicefee has not been paid, so the evaluation is not publicCDCB does not publish foreign bulls’ evaluations unless AI service fee has been paid, in order torespect the policies of individual countries.18 P a g e
The genotype is designated parentage verification only(PI “P”)Reference on Parentage verification codes: ervice/wiki/Parentage indicator codesThe bull is foreign, over 15months of age and no AI servicefee has been paidGenotyped U.S. males will receive a genomic evaluation monthly. Foreign genotyped malesreceive a genomic evaluation monthly up
Council on Dairy Cattle Breeding Navigation guide for Nominators Latest update: October 24th, 2017 . Purebreed Dariy Cattle Associations (PDCA), Dairy Records Processing Centers (DRPC), Dairy Record Providers (DRP), National Association of Animal Breeders (NAAB) and several
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Irish Cattle Breeding Industry. Co-ordinated by ICBF. -ICBF a "non-profit" co-operative of 30 cattle breeding organisations (AI, HB MRO's) 2 Farm Organisations. -Established in 2000. Industry now responsible for cattle breeding decisions. -Central database in 2002. Now key cornerstone of Irish AgFood industry.
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Table 3.2 Cattle holdings and average herd size by region, June 2017 2017 Change on year (%) England Average dairy herd size (head) 93 3.1 Average beef herd size (head) 27 1.1 Total cattle holdings Wales Average dairy herd size (head) N/A N/A Average beef herd size (head) N/A N/A Total cattle holdings Scotland Average dairy herd size (head) 96 .
Introduction to Academic Writing This study pack is designed to take about 50 minutes. It will give you an introduction to academic writing, sharing the most important principles that will guide you through writing during your degree at UCL. It was put together by the Writing Lab, which is the section of the Academic Communication Centre(ACC) that serves students from Bartlett; Psychology .
